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February 2014 Bioinformatics Papers of Note


Berry CC1, Bushman FD, et al.
Comparing DNA integration site clusters with scan statistics.
Bioinformatics. 2014 Feb 14. [Epub ahead of print]

Carin L, Lucas J, et al.
Bayesian joint analysis of heterogeneous genomics data.
Bioinformatics. 2014 Feb 21. [Epub ahead of print]

Monacell JT1, Carbone I.
Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics.
Bioinformatics. 2014 Feb 20. [Epub ahead of print]

Chen ZX, Chen KX, et al.
Multi-algorithm and multi-model based drug target prediction and web server.
Acta Pharmacol Sin. 2014 Feb 3. doi: 10.1038/aps.2013.153. [Epub ahead of print]

Al Mansoori S, Beatson SA, et al.
uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation.
BMC Bioinformatics. 2014 Feb 1;15:36. doi: 10.1186/1471-2105-15-36.

Bach F, Boeva V, et al.
SegAnnDB: interactive web-based genomic segmentation.
Bioinformatics. 2014 Feb 3. [Epub ahead of print]

Agostini F, Bolognesi B, et al.
The cleverSuite Approach for Protein Characterization: Predictions of Structural Properties, Solubility, Chaperone Requirements and RNA-Binding Abilities.
Bioinformatics. 2014 Feb 3. [Epub ahead of print]

Blake JA, Bianchi DW, et al.
DFLAT: functional annotation for human development.
BMC Bioinformatics. 2014 Feb 7;15:45. doi: 10.1186/1471-2105-15-45.

Eren AM, Huse SM, et al.
VAMPS: a website for visualization and analysis of microbial population structures.
BMC Bioinformatics. 2014 Feb 5;15:41. doi: 10.1186/1471-2105-15-41.

Gupta S, Panda B, et al.
SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.
BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.

Mielke CJ1, Mandarino LJ, Dinu V.
AMASS: a database for investigating protein structures.
Bioinformatics. 2014 Feb 26. [Epub ahead of print]

Burns KH, Halper-Stromberg E, et al.
Visualization and probability-based scoring of structural variants within repetitive sequences.
Bioinformatics. 2014 Feb 21. [Epub ahead of print]

Lao O, Liu F, Wollstein A, Kayser M.
GAGA: A New Algorithm for Genomic Inference of Geographic AncestryReveals Fine Level Population Substructure in Europeans.
PLoS Comput Biol. 2014 Feb 20;10(2):e1003480.

Jia P, Zhao Z.
VarWalker: Personalized Mutation Network Analysis of Putative CancerGenes from Next-Generation Sequencing Data.
PLoS Comput Biol. 2014 Feb 6;10(2):e1003460.

Colwill K, Creixell P, et al.
CoreFlow: A computational platform for integration, analysis and modeling of complex biological data.
J Proteomics. 2014 Feb 3. [Epub ahead of print]

Tuzhikov A, Panchin A, Shestopalov VI.
TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences.
Biotechnoiques 2014 Feb 1;56(2):78-84. doi: 10.2144/000114135.

Hatje K, Kollmar M.
Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes.
BMC Genomics. 2014 Feb 10;15:115. doi: 10.1186/1471-2164-15-115.

Barhdadi A, Dubé MP, et al.
Comparison of genotype clustering tools with rare variants.
BMC Bioinformatics. 2014 Feb 21;15(1):52. [Epub ahead of print]

Du R, Jin L, et al.
Evaluation of copy number variation detection for a SNP array platform.
BMC Bioinformatics. 2014 Feb 21;15(1):50. [Epub ahead of print]

Pullen N, Morris RJ.
Bayesian model comparison and parameter inference in systems biology using nested sampling.
PLoS One. 2014 Feb 11;9(2):e88419. doi: 10.1371/journal.pone.0088419.

Altay G, Kurt Z, Dehmer M, Emmert-Streib F.
Netmes: assessing gene network inference algorithms by network-based measures.
Evol Bioinform Online. 2014 Feb 6;10:1-9. doi: 10.4137/EBO.S13481.

Filed under

The Scan

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Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.